There's the scene where Rouge strangles Knuckles and yells at him for breaking the Master Emerald into pieces.
Rouge: What was that all about?! And LOOK WHAT YOU DID TO MY EMERALD!
Eggman's only response to Knuckles shattering the Emerald is to flail about as if he got punched...and let out a slightly disinterested Flat "What.", before pretty much shrugging his shoulders and heading back to base.
Three words: Amy. Hugging. Shadow. The look on his face is priceless. And you thought Rouge was terrifying.
Sonic Adventure 2, in the Dark Story before the Egg Golem boss. We get almost the same cutscene as when you fight it as Sonic, but in this version Sonic jumps up and delivers a kick to the golem which breaks the restraining mechanism on it and causes it to turn on Eggman. Though it's more of the dialogue that makes this hilarious:
Sonic: TERIAAAAA!!! Eggman: *When the Golem turns towards him* NOOOOOOOOOOO!
Made funnier by the fact that if you listen to it with the Japanese audio, it becomes "TEEEEEERIAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA!"
Knuckles: Oh no...the hatch door is open! Sonic:Don't sweat it, Knuckles. The only in the cargo bay are those Master Emerald pieces! Knuckles: What do you mean, don't sweat it?! Land the shuttle and let me out! Sonic: Knock it off, Knuckles! We're gonna crash this thing if you keep that up!
And then later, Sonic telling Eggman that Knuckles piloting the shuttle was a lot more dangerous than Eggman could ever be.
Sonic's recap of Crazy Gadget includes this line.
Sonic: Eggman said he'll trade us Amy for the Emerald... I have to think about that one!
After Shadow trashes The Biolizard in an epic one-on-one battle, he finishes with the greatest one-liner in the universe; "GET OUT, YOU UGLY PROTOTYPE!"
Omochao's reactions to getting hit can be pretty funny, especially when you weren't even the one who hit him and he still gets mad at you. Clearly, the programmers knew fans weren't gonna like him.
Basically, any moment when you're playing as Eggman, and take damage, sometimes he says "You! I'll make you pay for this!" He will say this when he takes damage from enemy attacks, running into enemies, even when he takes damage from a stage hazard, such as a spike, or a laser. What's funny there is the thought of him yelling at an inanimate object that didn't even intend to cause him any harm.
Sonic's second encounter with Shadow is supposed to be serious, but one simple error made it absolutely hilarious:
Sonic:I found you! Faker! Shadow: Faker? I think YOU'RE the fake hedgehog around here! You're comparing yourself to ME? Ha! You're not even good enough to be my f- Sonic:I'LL MAKE YOU EAT THOSE WORDS!
And speaking of which, just any time characters interrupting each other's sentence can qualify. Or hell, when Sonic speaks so fast he interrupts himself! "Hey! Its not his spee-he must be using the Chaos Emerald to wa-" "-name is Shadow."
Eggman catching the nightly news at his hideout.
"We interrupt this broadcawst for this impawtant news flawsh."
"Mysterio-YUSS-ly, the only thing stolen was-" "A Chaos Emerald???" "-a Chaos Emerald."
"Eyewitnesses on the scene identified the culprit as world-renowned hero, Sonic the Hedgehog." (this said over a ridiculously high-quality shot of a black hedgehog with red eyes and white fur who looks absolutely nothing like Sonic.) "Sounds more like the work ofShadow!"
Just the character's reaction to whenever a ghost pop ups from out of nowhere. They drop on the ground for a second and then get back on the ground again.
Debuggers have found ways to put Mech-less Eggman in other stages, mainly Sonic and Shadow stages. This is already funny on it's own, but then people discovered what happens when he gets an◊ upgrade in this form◊.
Try to get behind King Boom Boo too early... over and over again. "Rrr hrr, rrr hrr! Hee ha ha ha ha ha ha ha!"